Table 2 Performance of using different positional encoding conditions and DeepMHCII on BD2016
From: Structure-aware deep model for MHC-II peptide binding affinity prediction
Allele | DeepMHCII | Calibrated PE | Direct PE | ||||||
|---|---|---|---|---|---|---|---|---|---|
Pre (O) | Pre (T) | Post (O) | Post (T) | Pre (O) | Pre (T) | Post (O) | Post (T) | ||
AUC | 0.856 | 0.844 | 0.820 | 0.855 | 0.856 | 0.843 | 0.820 | 0.857 \(\uparrow\) | 0.855 |
PCC | 0.691 | 0.679 | 0.634 | 0.689 | 0.693\(\uparrow\) | 0.675 | 0.633 | 0.694 \(\uparrow\) | 0.692\(\uparrow\) |
SRCC | 0.682 | 0.672 | 0.630 | 0.681 | 0.687 \(\uparrow\) | 0.666 | 0.626 | 0.685\(\uparrow\) | 0.686\(\uparrow\) |
MSE | 0.0308 | 0.0301\(\downarrow\) | 0.0337 | 0.0312 | 0.0299 \(\downarrow\) | 0.0315 | 0.0341 | 0.0299 \(\downarrow\) | 0.0301\(\downarrow\) |